Taxonomy classification of blast output

Question

I am trying to do a taxonomic classification of my blast output, using scripts on this web-site https://github.com/bartaelterman/BlastTaxonomy. I am quite new to python and sometimes I try to find already existing scripts to do complicated jobs. However, scripts like this confuse me a lot. I have a very basic question, i.e. in the script below, where do I replace with my input file, can you give me a short explanation of the script like this to have an idea?

Also, if you have any other ideas how to do it, would be great!

import sys
sys.path.append("./scripts")
import blasthittaxonomy

def checkarguments():
    if len(sys.argv) != 2:
        print "usage: ./addTaxonomyToBlastOutput.py <blast output file>"
        sys.exit(-1)

def main():
    checkarguments()
    taxfetcher = blasthittaxonomy.TaxonomyFetcher()
    filename = sys.argv[1]
    infile = open(filename)
    header = infile.readline()
    print "\t".join(["seqnr", "hitginr", "hitname", "evalue", "bitscore", "similarity", "score",    "division", "scientificName", "rank1", "rank2"])
    for line in infile:
        newline = line.rstrip("\n")
        seqnr, ginr, hitname, evalue, bitscore, sim, score = newline.split("\t")
        division = ""
        scientName = ""
        rank1 = ""
        rank2 = ""
        if ginr != "":
        taxonomy = taxfetcher.getTaxonomy(int(ginr))
        if taxonomy != "":
            scientName = taxonomy[0]["ScientificName"]
            if scientName == "unidentified":
             scientName = ""
            else:
             division = taxonomy[0]["Division"]
             try:
                    rank1 = taxonomy[0]["LineageEx"][0]["ScientificName"]
             except:
             rank1 = ""
             try:
                    rank2 = taxonomy[0]["LineageEx"][1]["ScientificName"]
             except:
             rank2 = ""
    print "\t".join([seqnr, ginr, hitname, evalue, bitscore, sim, score, division, scientName, rank1, rank2])
taxfetcher.die()

main()

Answer 1

You don't replace anything, just run the script with your file name as a command-line argument

That's where the script reads the input file name:

filename = sys.argv[1]